Wade CM

References (4)

Title : Genome sequence, comparative analysis, and population genetics of the domestic horse - Wade_2009_Science_326_865
Author(s) : Wade CM , Giulotto E , Sigurdsson S , Zoli M , Gnerre S , Imsland F , Lear TL , Adelson DL , Bailey E , Bellone RR , Blocker H , Distl O , Edgar RC , Garber M , Leeb T , Mauceli E , MacLeod JN , Penedo MC , Raison JM , Sharpe T , Vogel J , Andersson L , Antczak DF , Biagi T , Binns MM , Chowdhary BP , Coleman SJ , Della Valle G , Fryc S , Guerin G , Hasegawa T , Hill EW , Jurka J , Kiialainen A , Lindgren G , Liu J , Magnani E , Mickelson JR , Murray J , Nergadze SG , Onofrio R , Pedroni S , Piras MF , Raudsepp T , Rocchi M , Roed KH , Ryder OA , Searle S , Skow L , Swinburne JE , Syvanen AC , Tozaki T , Valberg SJ , Vaudin M , White JR , Zody MC , Lander ES , Lindblad-Toh K
Ref : Science , 326 :865 , 2009
Abstract : We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.
ESTHER : Wade_2009_Science_326_865
PubMedSearch : Wade_2009_Science_326_865
PubMedID: 19892987
Gene_locus related to this paper: horse-1plip , horse-2plrp , horse-ACHE , horse-BCHE , horse-f6pri5 , horse-f6qlk6 , horse-f6qsc5 , horse-f6r958 , horse-f6sfg0 , horse-f6uif6 , horse-f6un85 , horse-f6vxp7 , horse-f6wfs9 , horse-f6wzv8 , horse-f6x0i7 , horse-f6x5e5 , horse-f6zmg7 , horse-f7afw6 , horse-f7agv7 , horse-f7bj10 , horse-f7bk45 , horse-f7bvl6 , horse-f7c7a8 , horse-f7cdt1 , horse-f7cxj0 , horse-f6ut17 , horse-f6svq9 , horse-f6xgj6 , horse-f6s101 , horse-f6wfa7 , horse-f7cpx3 , horse-f7adj7 , horse-f6r609 , horse-f6y0j2 , horse-f6zvb2 , horse-f7e4g0 , horse-f6ti02 , horse-f6re01 , horse-f6xmp6 , horse-f6vts1 , horse-f6quf7 , horse-f6tn81 , horse-f7bm46 , horse-f6q1u3 , horse-f6zna7 , horse-f6q208 , horse-f7cuh0 , horse-f6tq73 , horse-f6xa70 , horse-f6qj19 , horse-f6wgf3 , horse-f7d8t6 , horse-f6ul42 , horse-f7am73 , horse-f7dme2

Title : Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences - Mikkelsen_2007_Nature_447_167
Author(s) : Mikkelsen TS , Wakefield MJ , Aken B , Amemiya CT , Chang JL , Duke S , Garber M , Gentles AJ , Goodstadt L , Heger A , Jurka J , Kamal M , Mauceli E , Searle SM , Sharpe T , Baker ML , Batzer MA , Benos PV , Belov K , Clamp M , Cook A , Cuff J , Das R , Davidow L , Deakin JE , Fazzari MJ , Glass JL , Grabherr M , Greally JM , Gu W , Hore TA , Huttley GA , Kleber M , Jirtle RL , Koina E , Lee JT , Mahony S , Marra MA , Miller RD , Nicholls RD , Oda M , Papenfuss AT , Parra ZE , Pollock DD , Ray DA , Schein JE , Speed TP , Thompson K , Vandeberg JL , Wade CM , Walker JA , Waters PD , Webber C , Weidman JR , Xie X , Zody MC , Graves JA , Ponting CP , Breen M , Samollow PB , Lander ES , Lindblad-Toh K
Ref : Nature , 447 :167 , 2007
Abstract : We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.
ESTHER : Mikkelsen_2007_Nature_447_167
PubMedSearch : Mikkelsen_2007_Nature_447_167
PubMedID: 17495919
Gene_locus related to this paper: mondo-ACHE , mondo-b2bsf5 , mondo-b2bsz5 , mondo-BCHE , mondo-d2x2i6 , mondo-d2x2i8 , mondo-f6slk2 , mondo-f6wu00 , mondo-f6wuf2 , mondo-f6xfj4 , mondo-f6yt13 , mondo-f7c7p0 , mondo-f7ckd0 , mondo-f7cvq8 , mondo-f7cvr5 , mondo-f7eil6 , mondo-f7ez13 , mondo-f7f0i7 , mondo-f7fg16 , mondo-f7gcv7 , mondo-f7gep4 , mondo-f7gly2 , mondo-f6u7q2 , mondo-f7fw54 , mondo-f7dpf6 , mondo-f6pgj5 , mondo-f6yg68 , mondo-f7g8u4 , mondo-f7eyv1 , mondo-f6pq73 , mondo-f7cre0 , mondo-f7fdj0 , mondo-f7fdj5 , mondo-f7ft63 , mondo-f7ge99 , mondo-f7gea2 , mondo-f6pxq2 , mondo-f7awc1 , mondo-f7c412 , mondo-f7ev24 , mondo-f7b6s6 , mondo-f6vcx0 , mondo-f7g148 , mondo-f6tlv9 , mondo-f6tdm5 , mondo-f7f3w0 , mondo-f7fg39 , mondo-f7d6c2 , mondo-f6sdn0 , mondo-f7gi08 , mondo-f6xss6 , mondo-f6sa37 , mondo-f7gd97 , mondo-f6z6x9

Title : Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis - Kamper_2006_Nature_444_97
Author(s) : Kamper J , Kahmann R , Bolker M , Ma LJ , Brefort T , Saville BJ , Banuett F , Kronstad JW , Gold SE , Muller O , Perlin MH , Wosten HA , de Vries R , Ruiz-Herrera J , Reynaga-Pena CG , Snetselaar K , McCann M , Perez-Martin J , Feldbrugge M , Basse CW , Steinberg G , Ibeas JI , Holloman W , Guzman P , Farman M , Stajich JE , Sentandreu R , Gonzalez-Prieto JM , Kennell JC , Molina L , Schirawski J , Mendoza-Mendoza A , Greilinger D , Munch K , Rossel N , Scherer M , Vranes M , Ladendorf O , Vincon V , Fuchs U , Sandrock B , Meng S , Ho EC , Cahill MJ , Boyce KJ , Klose J , Klosterman SJ , Deelstra HJ , Ortiz-Castellanos L , Li W , Sanchez-Alonso P , Schreier PH , Hauser-Hahn I , Vaupel M , Koopmann E , Friedrich G , Voss H , Schluter T , Margolis J , Platt D , Swimmer C , Gnirke A , Chen F , Vysotskaia V , Mannhaupt G , Guldener U , Munsterkotter M , Haase D , Oesterheld M , Mewes HW , Mauceli EW , Decaprio D , Wade CM , Butler J , Young S , Jaffe DB , Calvo S , Nusbaum C , Galagan J , Birren BW
Ref : Nature , 444 :97 , 2006
Abstract : Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence strategies to kill its host. U. maydis belongs to the group of biotrophic parasites (the smuts) that depend on living tissue for proliferation and development. Here we report the genome sequence for a member of this economically important group of biotrophic fungi. The 20.5-million-base U. maydis genome assembly contains 6,902 predicted protein-encoding genes and lacks pathogenicity signatures found in the genomes of aggressive pathogenic fungi, for example a battery of cell-wall-degrading enzymes. However, we detected unexpected genomic features responsible for the pathogenicity of this organism. Specifically, we found 12 clusters of genes encoding small secreted proteins with unknown function. A significant fraction of these genes exists in small gene families. Expression analysis showed that most of the genes contained in these clusters are regulated together and induced in infected tissue. Deletion of individual clusters altered the virulence of U. maydis in five cases, ranging from a complete lack of symptoms to hypervirulence. Despite years of research into the mechanism of pathogenicity in U. maydis, no 'true' virulence factors had been previously identified. Thus, the discovery of the secreted protein gene clusters and the functional demonstration of their decisive role in the infection process illuminate previously unknown mechanisms of pathogenicity operating in biotrophic fungi. Genomic analysis is, similarly, likely to open up new avenues for the discovery of virulence determinants in other pathogens.
ESTHER : Kamper_2006_Nature_444_97
PubMedSearch : Kamper_2006_Nature_444_97
PubMedID: 17080091
Gene_locus related to this paper: ustma-q4p4j7 , ustma-q4p5d2 , ustma-q4p8h8 , ustma-q4p8x7 , ustma-q4p082 , ustma-q4p194 , ustma-q4pa07 , ustma-q4pas0 , ustma-q4pbb4 , ustma-q4pg48

Title : Genome sequence, comparative analysis and haplotype structure of the domestic dog - Lindblad-Toh_2005_Nature_438_803
Author(s) : Lindblad-Toh K , Wade CM , Mikkelsen TS , Karlsson EK , Jaffe DB , Kamal M , Clamp M , Chang JL , Kulbokas EJ, 3rd , Zody MC , Mauceli E , Xie X , Breen M , Wayne RK , Ostrander EA , Ponting CP , Galibert F , Smith DR , deJong PJ , Kirkness E , Alvarez P , Biagi T , Brockman W , Butler J , Chin CW , Cook A , Cuff J , Daly MJ , Decaprio D , Gnerre S , Grabherr M , Kellis M , Kleber M , Bardeleben C , Goodstadt L , Heger A , Hitte C , Kim L , Koepfli KP , Parker HG , Pollinger JP , Searle SM , Sutter NB , Thomas R , Webber C , Baldwin J , Abebe A , Abouelleil A , Aftuck L , Ait-Zahra M , Aldredge T , Allen N , An P , Anderson S , Antoine C , Arachchi H , Aslam A , Ayotte L , Bachantsang P , Barry A , Bayul T , Benamara M , Berlin A , Bessette D , Blitshteyn B , Bloom T , Blye J , Boguslavskiy L , Bonnet C , Boukhgalter B , Brown A , Cahill P , Calixte N , Camarata J , Cheshatsang Y , Chu J , Citroen M , Collymore A , Cooke P , Dawoe T , Daza R , Decktor K , DeGray S , Dhargay N , Dooley K , Dorje P , Dorjee K , Dorris L , Duffey N , Dupes A , Egbiremolen O , Elong R , Falk J , Farina A , Faro S , Ferguson D , Ferreira P , Fisher S , FitzGerald M , Foley K , Foley C , Franke A , Friedrich D , Gage D , Garber M , Gearin G , Giannoukos G , Goode T , Goyette A , Graham J , Grandbois E , Gyaltsen K , Hafez N , Hagopian D , Hagos B , Hall J , Healy C , Hegarty R , Honan T , Horn A , Houde N , Hughes L , Hunnicutt L , Husby M , Jester B , Jones C , Kamat A , Kanga B , Kells C , Khazanovich D , Kieu AC , Kisner P , Kumar M , Lance K , Landers T , Lara M , Lee W , Leger JP , Lennon N , Leuper L , LeVine S , Liu J , Liu X , Lokyitsang Y , Lokyitsang T , Lui A , MacDonald J , Major J , Marabella R , Maru K , Matthews C , McDonough S , Mehta T , Meldrim J , Melnikov A , Meneus L , Mihalev A , Mihova T , Miller K , Mittelman R , Mlenga V , Mulrain L , Munson G , Navidi A , Naylor J , Nguyen T , Nguyen N , Nguyen C , Nicol R , Norbu N , Norbu C , Novod N , Nyima T , Olandt P , O'Neill B , O'Neill K , Osman S , Oyono L , Patti C , Perrin D , Phunkhang P , Pierre F , Priest M , Rachupka A , Raghuraman S , Rameau R , Ray V , Raymond C , Rege F , Rise C , Rogers J , Rogov P , Sahalie J , Settipalli S , Sharpe T , Shea T , Sheehan M , Sherpa N , Shi J , Shih D , Sloan J , Smith C , Sparrow T , Stalker J , Stange-Thomann N , Stavropoulos S , Stone C , Stone S , Sykes S , Tchuinga P , Tenzing P , Tesfaye S , Thoulutsang D , Thoulutsang Y , Topham K , Topping I , Tsamla T , Vassiliev H , Venkataraman V , Vo A , Wangchuk T , Wangdi T , Weiand M , Wilkinson J , Wilson A , Yadav S , Yang S , Yang X , Young G , Yu Q , Zainoun J , Zembek L , Zimmer A , Lander ES
Ref : Nature , 438 :803 , 2005
Abstract : Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
ESTHER : Lindblad-Toh_2005_Nature_438_803
PubMedSearch : Lindblad-Toh_2005_Nature_438_803
PubMedID: 16341006
Gene_locus related to this paper: canfa-1lipg , canfa-2neur , canfa-3neur , canfa-ACHE , canfa-BCHE , canfa-cauxin , canfa-CESDD1 , canfa-e2qsb1 , canfa-e2qsl3 , canfa-e2qsz2 , canfa-e2qvk3 , canfa-e2qw15 , canfa-e2qxs8 , canfa-e2qzs6 , canfa-e2r5t3 , canfa-e2r6f6 , canfa-e2r7e8 , canfa-e2r8v9 , canfa-e2r8z1 , canfa-e2r9h4 , canfa-e2r455 , canfa-e2rb70 , canfa-e2rcq9 , canfa-e2rd94 , canfa-e2rgi0 , canfa-e2rkq0 , canfa-e2rlz9 , canfa-e2rm00 , canfa-e2rqf1 , canfa-e2rss9 , canfa-f1p6w8 , canfa-f1p8b6 , canfa-f1p9d8 , canfa-f1p683 , canfa-f1pb79 , canfa-f1pgw0 , canfa-f1phd0 , canfa-f1phx2 , canfa-f1pke8 , canfa-f1pp08 , canfa-f1ppp9 , canfa-f1ps07 , canfa-f1ptf1 , canfa-f1pvp4 , canfa-f1pw93 , canfa-f1pwk3 , canfa-pafa , canfa-q1ert3 , canfa-q5jzr0 , canfa-e2rmb9 , canlf-f6v865 , canlf-e2rjg6 , canlf-e2r2h2 , canlf-f1p648 , canlf-f1pw90 , canlf-j9p8v6 , canlf-f1pcc4 , canlf-e2qxh0 , canlf-e2r774 , canlf-f1pf96 , canlf-e2rq56 , canlf-j9nwb1 , canlf-f1ptw2 , canlf-j9p8h1 , canlf-e2ree2 , canlf-f1prs1 , canlf-j9nus1 , canlf-e2rf91 , canlf-f1pg57 , canlf-f1q111